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Enable pathway analysis over PC loadings in fpcaAnalysis shiny module #27

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lianos opened this issue Mar 21, 2020 · 0 comments
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enhancement New feature or request

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lianos commented Mar 21, 2020

We already can run GSEA over the loadings of individual dimension using a code driven analysis ...

library(multiGSEA)
library(FacileAnalysis)

gdb <- getMSigGeneSetDb("reactome", species = "human", id.type = "entrez")

pca.crc <- FacileData::exampleFacileDataSet() %>%
  FacileData::filter_samples(indication == "CRC") %>%
  fpca()

pca.gsea <- ffsea(pca.crc, gdb, dim = 1)

... and we want to be able to do this using the shiny gadget mojo.

We either want to:

  1. Expose this functionality in the fpcaAnalsys shiny module.
  2. Create a derivitave shiny analysis module that takes the output of the fpcaAnalaysis
    module, and enables user to configure a GSEA run along one of its dimensions.
@lianos lianos added the enhancement New feature or request label Mar 21, 2020
@lianos lianos self-assigned this Mar 21, 2020
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